What mixture of “design” and “evolution” is possible as the IDM collapses?

This offers the simplest “neutral” colloquial mixture of “design” and “evolution” that I’ve seen in a long time. The site is no longer maintained, but the language persists.

“As a designer it is important to understand where design came from, how it developed, and who shaped its evolution. The more exposure you have to past, current and future design trends, styles and designers, the larger your problem-solving toolkit. The larger your toolkit, the more effective of a designer you can be.” http://www.designishistory.com/this-site/

Here, the term “evolution” as used just meant “history”. The author was not indicating “design theory evolution”, but rather instead the “history of designs” themselves, which have been already instantiated.

The topic “design is history” nevertheless enables an obvious point of contact between “evolution” and “design”. They both have histories that can be studied. Present in the above meaning of “design” are the origin, processes and agent(s) involved in the “designing”. This differs significantly from the Discovery Institute’s version of “design theory”, when it comes to history, aim, structure and agency, since the DI’s version flat out avoids discussion of design processes and agent(s). The primary purpose of the DI’s “design theory”, meanwhile, is USAmerican religious apologetics and “theistic science”.

The quotation above likely didn’t come from an IDist, and it isn’t referencing “Intelligent Design” theory as a supposed “scientific theory”. The “designer” in the quotation above is a (more or less intelligent) human designer, not a Divine Designer. This fact distinguishes it “in principle” from the Discovery Institute’s ID theory, which is supposed to be (depends on who you’re speaking with in the IDM) about first biology, then informatics, and statistics. The DI’s ID theory is not actually focused on “designing by real designers”, but rather on apologetics using “design” and informational probabilism.

The Discovery Institute’s failure to distinguish or even highlight the differences and similarities between human design and Divine Design, and instead their engagement in active distortion, equivocation, double-talking, and obfuscation between them, are marks of its eventual downward trend to collapse.

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1,506 thoughts on “What mixture of “design” and “evolution” is possible as the IDM collapses?

  1. Alan Fox to Kantian Naturalist: Well, what is meant by a mind. I think of it as what my brain does

    When you say ‘I think’, what do you mean by ‘I’ ? How did you discover that you had a brain in the first place?

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  2. Neil Rickert to Kantian Natuuralist: I think it better to say that minds don’t really exist

    I’ll ask you the same as I asked Alan. When you say ‘I think’, what do you mean by ‘I’ ? How did you discover that you had a brain in the first place?

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  3. Alan Fox:

    Kantian Naturalist: mental illness

    One of my pet peeves. Psychological disorders are no less physical than any other illness.

    How do you account for the placebo effect?

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  4. Neil Rickert:

    Kantian Naturalist: I don’t see how one could gerrymander language so that “mental” is OK as an adjective but “mind” is prohibited as a noun.

    I do think of the term “mental states” as absurd.

    It’s all to do with what frame of mind you are in 🙂

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  5. Flint: So maybe quarks never actually formed, and all the universe’s matter was present from the instant of the bang.

    Quarks are purely mathematical entities.

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  6. Allan Miller:

    CharlieM: I don’t reject the fact that DNA gets transmitted. I would reject the proposal that genes transmit themselves through the generations.

    Reject all you like, that is pretty much what happens. Of course the genes that specifically do that – DNA polymerases and their adjuncts – are but a fragment of the total genome.

    It is cellular processes which govern genetic activity. Molecular complexes supplied by the parent begin the processes of cell division and development of the offspring. DNA polymerase, helicase, single stranded binding protein, DNA topoisomerase, primase, and ligase all work together to achieve this development. The order of their construction is indeed contained in the genome but various sequences still need to be selected and manipulated in time and space.

    DNA polymerase has the remarkable ability to add bases at one thousand per second and it also removes errors and add correct bases. It does this in conjunction with many other protein complexes.

    These are the processes that get passed on from generation to generation.

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  7. Allan Miller: Nonetheless, this does not actually address the quote of mine that it purports to address. Common genetic descent is a thing. You share ‘common genetic descent’ with your parents, and back through the generations with coalescent ancestors. We know the mechanism(s). It is that which you ‘reject’ in believing that a common trait does not, in fact, result from a common genetic origin, not whether genes can be said to be active or passive actors in the process.

    I don’t deny that genes get passed on. But genes are just one part of the whole organism and it is whole organisms that get passed on. That humans have tens of thousands of genes but hundreds of thousands of different proteins makes obvious the importance of gene manipulation.

    (I’m just back off (another) holiday, and see you’ve been wading through my many historic utterances in my absence. For funzies, I might work backwards … we probably will not meet in the middle)

    Hope your genes enjoyed their holiday 🙂

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  8. CharlieM: I’ll ask you the same as I asked Alan. When you say ‘I think’, what do you mean by ‘I’ ? How did you discover that you had a brain in the first place?

    I assume that there is some point to this question. But I don’t know what that point is.

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  9. CharlieM: I do think of the term “mental states” as absurd.

    It’s all to do with what frame of mind you are in 🙂

    If the term “mental state” had to do with current frame of mind, that would at least make sense. However philosophers say that beliefs are states of mind, even when those are beliefs that they ascribe to me, but which have nothing to do with my current thoughts.

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  10. CharlieM,

    I think you have the map mixed with the territory. Physicists have produced mathematical models to explain and predict the observed behaviour of fundamental particles.

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  11. CharlieM:

    One of my pet peeves. Psychological disorders are no less physical than any other illness.

    How do you account for the placebo effect?

    As far as it exists, perhaps thinking you are going to get better has a positive effect on getting better. Not sure how that relates to diseases such as schizophrenia being physical.

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  12. CharlieM: Me: Reject all you like, that is pretty much what happens. Of course the genes that specifically do that – DNA polymerases and their adjuncts – are but a fragment of the total genome.

    Charlie: It is cellular processes which govern genetic activity. Molecular complexes supplied by the parent begin the processes of cell division and development of the offspring.

    Supplied by the parental genome. Endless recasting in terms you find more congenial does not change that basic fact of biology. You say it, I refute it, you say it again, round and round … I’m happy to play this game because I’m stubborn, and because I’m right! Your recasting it yet again changes no facts of biology. It may be persuasive to you, but you’re trying to persuade someone else, by simple repetition.

    You appear to be trying to refute reductionism through obscurantism – by holding your telescope to the wrong eye and deliberately not seeing the information flow, by mashing ‘phenotype’ into a vague whole such that genes become subordinate to it. Because vague-phenotype extracts genetic sequence, and vague-phenotype replicates DNA, and vague-phenotype controls cell division and apoptosis, then it’s all about vague-phenotype. Something that is both a property of a single zygote, and a massed collection of descendants of that zygote. When a cell, that cell ‘manipulates its genome’. When a collection, the whole collection ‘manipulates its genome(s)’.

    But in fact, each component is specific-genotype. A separate part of genotype in each case, not a vague composite. The genome is a collective of specialisms; a mini-society (the whole reflected in the parts, hee hee). It multiplies, but ultimately it’s a single (haploid) copy that pops out.

    DNA polymerase, helicase, single stranded binding protein, DNA topoisomerase, primase, and ligase all work together to achieve this development. The order of their construction is indeed contained in the genome but various sequences still need to be selected and manipulated in time and space.

    And all of that is also contained in the genome. Which is why the zygote of a particular species ends up replicating into an organism with a roughly consistent form, behaviour, developmental progression, response. That information is not in ‘the cell’; it’s in the genome. Demonstrably.

    DNA polymerase has the remarkable ability to add bases at one thousand per second and it also removes errors and add correct bases.

    All specified within the genetic sequence of the enzyme.

    It does this in conjunction with many other protein complexes.

    Whose sequence and control resides in the genome.

    These are the processes that get passed on from generation to generation.

    In the genome.

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  13. CharlieM: I don’t deny that genes get passed on. But genes are just one part of the whole organism and it is whole organisms that get passed on.

    That is incorrect. A whole beaver does not pass on its whole-beaverness; a tiny beaver that grows into a new one. It passes on its genes, plus, for a moment, a handful of gene products generated by the parental genome, before the offspring genome starts generating them directly.

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  14. Corneel:

    CharlieM: asks Allan: What do you mean by group transmittion?

    Allan: The mechanism by which a trait becomes shared by a clade. Common genetic descent is the usual one. You reject that (sometimes), so must mean something else. How does it work?

    Charlie: I don’t reject the fact that DNA gets transmitted. I would reject the proposal that genes transmit themselves through the generations.

    That doesn’t work. DNA doesn’t get transmitted to the entire species/kind/group, so cannot explain how groups remain homogeneous. Allan asked for the mechanism that broadcasts novel traits to the entire group.

    What I write below I do not offer as facts but as me giving my understanding from my personal thoughts and beliefs.

    Nothing needs to get broadcast because the group already has the potential to express the archetype which encompasses all of the novelties. Individual circumstances limit this expression.

    The concept oft mechanism applies to the physical organisation alone. But there is much more to organisms over and above the physical body. There are higher organisational principles with their own laws. It is a mistake to apply the mechanical laws in which cause precedes effect to these higher principles. The life organisation is rhythmic in character with self-generated movement. Further we have the sentient organisation and the ego organisation with their own specific laws. Similarly, the laws of water are different from and not contained in the laws of hydrogen nor the laws of oxygen. Our egos have their own laws which cannot be arrived at through physics and chemistry.

    Thoughts are not physical but they are just as real as physical substance. Thinking is an activity of the ego and it is only in the human that the ego has condensed to the point where it aligns with the physical individual.

    In addition, to give some weight to your denial that genes “transmit themselves”, you still need to deal with parasitic DNA elements in some other way than turning a blind eye to them. You rely on observation , remember?

    Chromosomes are intricate, living, moving, complex molecules consisting of more than strings of nucleotides. What is the chemical composition of these ‘parasitic DNA elements’? I think you’ll find that DNA is only one of the constituents and would be meaningless outwith the complex of which it forms a vital part..

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  15. Allan Miller:

    Corneel:
    In addition, to give some weight to your denial that genes “transmit themselves”, you still need to deal with parasitic DNA elements in some other way than turning a blind eye to them. You rely on observation , remember?

    I followed the link and read onwards for a few comments, and found this by me. Evidently I’d already said similar several times already, even then. It contains the essence of my twin mantras: that the protein sequences supposedly ‘acting upon’ the genome nonetheless derive from it, and that the evolutionary argument on subgenome levels of selection shouldn’t be confused with a physiological one on gene expression. Add my trademark dose of sarcasm, and you have the essence of every post I’ve written on this matter! I think I’ll just link it in future: saves finger-ends.

    The only time that the DNA molecule is observed to be in isolation is when human researchers separate it out of the living substance. In your mind you see DNA and proteins as separate but they are never seen as such in living systems. Together they have the properties of life, separate them and you end up with dead matter.

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  16. CharlieM: But there is much more to organisms over and above the physical body. There are higher organisational principles with their own laws. It is a mistake to apply the mechanical laws in which cause precedes effect to these higher principles. The life organisation is rhythmic in character with self-generated movement. Further we have the sentient organisation and the ego organisation with their own specific laws.

    Could you explicitly state what those laws are and explain how they describe the relationship between archetype and phenotype? How does the potential for a novel trait become expressed by all the members of a clade, but not outside it? I don’t believe you’ve answered Allan’s original question.

    CharlieM: Chromosomes are intricate, living, moving, complex molecules consisting of more than strings of nucleotides. What is the chemical composition of these ‘parasitic DNA elements’? I think you’ll find that DNA is only one of the constituents and would be meaningless outwith the complex of which it forms a vital part.

    Parasites tend to be meaningless without a host, sure. That is their nature. But it is folly to argue that parasites are part of the host organism. The same goes for parasitic DNA elements: they do not serve the interests of the organism or the chromosome that hosts them.

    You ran into this issue before, when we were discussing viruses. You tried to deal with this by pointing out that viruses are harmless without a host, which is like saying that volcanic eruptions are perfectly safe provided that you are at not around to experience its consequences. That is just evasion of the inconvenient fact you were asked to confront. Viruses and other parasitic elements are pathogens that clearly do not exist for our benefit, but have their own agenda.

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  17. Corneel:

    Allan Miller: Evidently I’d already said similar several times already, even then.

    Perhaps you need to use a more extreme form of that argument.

    I think the problem lies in treating genes as agents. Individual organisms are agents, even intra-cellular complexes such as dynein ‘motors’ and chromosomes can be classed as agents. But unless genes are defined as more than just sequences of DNA then they are not productive agents.

    Look at the multitude of cell types in multicellular eukaryotes. The DNA remains the same but the way it is arranged is highly variable. The spatial localisation of chromosome territories and how different areas are moved into close proximity with one another affect gene expression. Regulated activity is highly variable depending on cell type. Cells manipulate their DNA in a way reminiscent of how some invertebrates manipulate their silk, .with great precision and purpose.

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  18. CharlieM: The only time that the DNA molecule is observed to be in isolation is when human researchers separate it out of the living substance.

    I’ve done this. Briefly, precipitation with phenol is the method. The strands, still well hydrated, can be gathered on a glass rod. The strands align vertically under the effects of gravity, hydrogen bonding, surface tension into one composite strand with the most fascinating banded optical effect.

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  19. CharlieM: I think the problem lies in treating genes as agents. Individual organisms are agents, even intra-cellular complexes such as dynein ‘motors’ and chromosomes can be classed as agents.

    You are, perhaps without realising it, (re-)making the distinction between genotype and phenotype. No need to reinvent the wheel.

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  20. CharlieM: Cells manipulate their DNA in a way reminiscent of how some invertebrates manipulate their silk, .with great precision and purpose.

    Really bad analogy!

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  21. Alan Fox:

    Corneel: Allan asked for the mechanism that broadcasts novel traits to the entire group.

    It’s sex, isn’t it?

    Corneel: I doubt it. Charlie insists on groups developing certain “passions” but I think he means something else.

    Sex and reproduction are very interestring areas of study. All animals get the urge to have sex but only humans recognise the consequences of these acts.

    Lower animals let Mother Nature supply the womb in which their offspring begin their development, with even fertilisation taking place in the wider environment. For higher animals this becomes a process taking place within the bodies of individuals and even after parturition the offspring is still nourished from the body of the mother. Responsibility for the care and development of offspring has moved increasingly from Mother Nature to the individual mother. Sex in animals is an instinctive affair quite often governed by the seasons and the participants can do very little about changing the course of what follows. On the other hand, for humans, we have been able to separate sex from reproduction and have the power to enjoy sex while preventing the natural consequences.

    This is one demonstration of our evolutionary trajectory in the emancipation from nature. We can still be bound by our passions but at least we have gained a little freedom in that we can control their consequences to some extent.

    Animals of the same kind show a great uniformity in their sexual behaviour. Humans show a great deal more individuality in this.

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  22. Allan Miller:

    Corneel: Perhaps you need to use a more extreme form of that argument.

    Not sure what form that might take!

    I think Charlie’s ‘holism’ is better named ‘fuzzism’. If the genetic detail can be rendered in vague enough terms, by sleight of hand the role of genes, elucidated by reduction, becomes magically subordinated to the vague requirements of a ‘system’. For lo, ‘genes’, in the general sense, cannot be expressed without ‘the system’, in the general sense

    I don’t see what is so vague about the system that is a chromosome.

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  23. Corneel:

    Allan Miller: I think Charlie’s ‘holism’ is better named ‘fuzzism’.

    No, it is more akin to prose poetry. Just look at it:

    CharlieM: Truth is a unity and it is because of the way in which we are constituted that entities which are connected are at first perceived by us as separate. Knowledge is the process by which connections are made and unity is restored.

    That’s friggin’ beautiful. Pity it is completely hollow.

    A flute is just a hollow tube to the spider that ventures up it.

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  24. CharlieM: Sex and reproduction are very interestring areas of study.

    Way to miss the point. Sex is evolution’s biggest idea. It’s the halving, swapping and shuffling of genomes allowing and promoting the proliferation of novel genomes that is important. The rest is window dressing.

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  25. Allan Miller:

    CharlieM:
    You have shifted position from talking about genes acting to talking about genomes acting. I would say that this is a step in the right direction.

    I haven’t. I do find odd notions being attributed to me. The genome ‘acts’ via the effect of subsections thereof – genes

    And the Irish dancers act by means of their legs.

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  26. Allan Miller:

    Maybe we can come to a mutual understanding of what is meant by ‘gene’

    It varies somewhat – in the discussion that followed this comment, Corneel advanced the gene=product view favoured by molecular biologists. So a ‘gene’ would produce either a functional RNA directly, or an mRNA which further processing would translate into a protein. But when Dawkins talks of ‘Selfish Genes’, he is not using that definition, but the broader one coined by George Williams: simply, any segment of a genome with a significant degree of evolutionary persistence independent of neighbouring units. That ‘independent persistence’ is effected, in cyclically haplodiploid eukaryotes, by iterated recombination at the end of the diploid phase. It slices genomes into subunits that integrate into the genomes of the future population, and it is those ‘persistent segments’ that a gene-centrist is interested in.

    They couldn’t give a tuppenny fig if these genome segments ‘act’, are ‘acted upon’, or whatever other semantic tomfoolery one wishes to import. What counts is the correlation with organismal fitness of such a segment (typically measured as mean offspring of carriers vs non-carriers). This is what justifies the choice of ‘the gene’ (so defined) as a unit of selection below that of the organism. The – ahem – whole reflected in the parts. It should be right up your street.

    I have no problem with the correlations you highlight. It’s when the correlations become causations that is what I take issue with.

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  27. CharlieM: [Snip exasperated riff by me about how many times I find myself dealing with the same points repeated …]
    Charlie: The only time that the DNA molecule is observed to be in isolation is when human researchers separate it out of the living substance.

    Ye Gods. Your response is repetition again? I’ll say it again with block capitals and italics for emphasis: IT DOESN’T MATTER. It really doesn’t. See #1. Gene centrism is not dependent on the observation of naked DNA. I wrote that on 4th August. It’s now 5th September.

    In your mind you see DNA and proteins as separate but they are never seen as such in living systems.

    They are separate, even in living systems. Of course they are separate; they’re a completely different class of molecule, with different functions. Nonetheless, every protein sequence is in DNA. Most of them are less than a day old, and must be refreshed from the genome. Every control region is rooted in DNA. All of ’em. You are attempting to refute reductionism by wielding ignorance of detail; raising that to the level of fundamental principle.

    Together they have the properties of life, separate them and you end up with dead matter.

    Because the modern genome acts through (inter alia) the extensive production of proteins. This is not a sensible objection to gene centrism. As I have also observed before: you think gene centrists don’t know any biology?

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  28. CharlieM:
    I don’t see what is so vague about the system that is a chromosome.

    Haha. “I don’t see what is so vague about [says something vague]” 😁

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  29. CharlieM:
    I have no problem with the correlations you highlight. It’s when the correlations become causations that is what I take issue with.

    Genes clearly have a causal relationship with form. That’s well established; it’s not mere ‘correlation’. This causal relationship does not disappear with the observation that genes must be expressed to have effect (an inevitable corollary of the commonly-used definition of ‘gene’). So, your problem appears to be pretty fundamental: you take issue with the entire science of genetics.

    Genetic differences also clearly can have a causal effect on organismal success. So again you seem to have a bit of an issue with the entire science of evolutionary biology.

    Other than that, it’s all good, I presume!

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  30. CharlieM: Corneel: Perhaps you need to use a more extreme form of that argument.

    Charlie:I think the problem lies in treating genes as agents.

    Your problem is with a metaphor, then.

    Look at the multitude of cell types in multicellular eukaryotes. The DNA remains the same but the way it is arranged is highly variable. […] Regulated activity is highly variable depending on cell type.

    You’ll note that these complexities are repeated, over and over, in every organism you choose to examine from a species, to the extent that one can generalise from a few instances. Why is that? What ensures this consistency of expression throughout differentiation and development, across an entire population? It can’t be proteins; they turn over rapidly, in a matter of hours. You could waft vaguely at something undemonstrable, acting by means obscure. Or, you could drop your resistance to the concept and consider the role of genetics.

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  31. CharlieM,

    Nothing needs to get broadcast because the group already has the potential to express the archetype which encompasses all of the novelties. Individual circumstances limit this expression.

    I don’t see how a novel genetic instance – say an oak – gets to access its oak ‘archetype’. Haploid pollen and ovule come together to form a diploid cell. It divides; in my conception differential gene expression causes leaf and trunk and acorn to develop from the descendants of this totipotent cell. But you don’t think differential gene expression is enough of an explanation. Something is channelling and constraining the development of the oak, interacting in some way with genetic expression or broader form, if genetic expression is itself insufficient to generate full-on ‘oakiness’. I struggle to conceptualise how this additional force might operate, starting with haploid cells.

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  32. CharlieM: I think the problem lies in treating genes as agents. Individual organisms are agents, even intra-cellular complexes such as dynein ‘motors’ and chromosomes can be classed as agents. But unless genes are defined as more than just sequences of DNA then they are not productive agents.

    No, I do not think that is an issue. In my book, agents are conscious beings capable of acting with intent. Neither proteins, protein complexes, cells, chromosomes nor genes fit the bill.

    My assesment is that part of the problem lies in your view of all matter as being passive and inert, ignoring its chemical properties and capacity for self organization. The other issue is your failure to appreciate the central role of heritable variation for evolutionary change.

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  33. CharlieM: A flute is just a hollow tube to the spider that ventures up it.

    … and it is too narrow for her to weave her web there.

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  34. Allan Miller:
    CharlieM,

    As to your Halfmann quote, this is NOT ‘orthogonal to the central dogma of molecular biology’. Unless it involves reverse translation, which it doesn’t. People claim on a daily basis that the dogma is under threat. People thereby prove on a daily basis that they don’t know what it states.

    He said these processes are othogonal to the dogma not in opposition to it and so it does not have to involve reverse translation. Control is from above the level of the gene. Here is a link to his lab ‘site. The opening paragraph includes this:

    We have discovered that clonal populations of multicellular budding yeast exhibit a rich diversity of cooperative behaviors.

    They are investigating the control of protein conformational changes not governed by the genome. I would say that alternative splicing displays a similar level of control not governed by the genome. Also this videoI have linked to previously is more reminiscent of field dynamics rather than control from point sources within each nucleus. It shows a stage in the process of drosophila embryo formation.

    And of course this is just one piece of research from many that Talbott mentions. There is much more there that we could discuss and argue about.

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  35. Allan Miller:

    To say that everything is controlled by the genes is a gross simplification that does not come close to the reality of the situation.

    Do you think ‘everything is controlled by the system’ is somehow superior in that regard?

    Yes. We humans are beginning to take over responsibility for controlling what at
    one time nature had sole control of. We are conscious systems that have some control over genes. They were under the control that natural systems before we gained the power we now hold, and to a great extent natural systems are still in control. In labs genes do not control model organisms: living, thinking, communicating human beings do. Scientists decide the fate of the organisms under study. Scientists are not just collections of genes, they are unified systems.

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  36. CharlieM,

    So glad to see you reference Eric Wieschaus; he and Christiane Nüsslein-Volhard developed the famous Heidelberg Screen: by surrounding the embryos with screens made of different elements, they were able to prevent the embryos from accessing different specific aspects of the fruit fly archetype.
    The bicoid aspect, the Krüppel aspect (one of the gap aspects of the archetype) the pair rule, and the segment polarity archetype.
    [finger to earpiece] What do you mean, “not that kind of screen”?

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  37. CharlieM: He said these processes are othogonal to the dogma not in opposition to it and so it does not have to involve reverse translation.

    Still no. Not ‘orthogonal’ to it either (such a pretentious word when used in such a way, I find). What does that even mean? If the dogma is not challenged, why mention it?

    Control is from above the level of the gene.

    It’s arguably ‘above the level’ of any given gene (depending on definition), but it is still part of the heritable material – DNA – and not elsewhere. This is still not a valid objection to gene-centrism. Each gene would not have to do everything itself before gene centrism could gain any traction. See #2. I find myself nonplussed even having to type this out – as if gene-centrists ever imagined that each gene acted alone, till Talbott et al came along!

    As to the genetic basis of control itself, I went into this in some detail. If you can find an exception to the rule that control ultimately resides in DNA, I’d be interested to hear it. But make sure it really is an exception, and not an artefact of your failure to follow the causal chain.

    The opening paragraph includes this: “we have discovered that clonal populations of multicellular budding yeast exhibit a rich variety of cooperative behaviours”

    An important keyword there is ‘clonal’. Care to have a stab as to why I’d say that?

    They are investigating the control of protein conformational changes not governed by the genome. I would say that alternative splicing displays a similar level of control not governed by the genome.

    You would be dead wrong. How else does a tissue-specific isoform arise consistently in every member of a species, if not under genetic control?

    Again, you’re attaching limpet-like to the work of people you perceive as ‘revolutionaries’ without troubling to learn the basics, or follow the counterargument.

    And of course this is just one piece of research from many that Talbott mentions. There is much more there that we could discuss and argue about.

    You’d be better learning to walk. You are impressed by apparent paradigm shifts, which you swallow uncritically. But there’s a reason the likes of Talbott are not widely proclaimed as visionaries in biological circles.

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  38. CharlieM:Me: Do you think ‘everything is controlled by the system’ is somehow superior in that regard?

    Charlie: Yes. We humans are beginning to take over responsibility for controlling what atone time nature had sole control of.

    Who mentioned humans? Oh, you did. Again. It’s all you care about; the rest of biology is just so much fluff.

    We are conscious systems that have some control over genes. They were under the control that natural systems before we gained the power we now hold, and to a great extent natural systems are still in control. In labs genes do not control model organisms: living, thinking, communicating human beings do. Scientists decide the fate of the organisms under study. Scientists are not just collections of genes, they are unified systems.

    I think this is a rather poor justification of the preferential use of the term ‘everything is controlled by the system’ wrt biology. How about pre 1950? Did we only become ‘systems’ when we became aware of DNA? Or was it in the Pleistocene, with primitive domestication?

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  39. Allan Miller: Righto, I’m caught up. I’ve been away in the far North-West of Scotland, contemplating the passions of midge and tick for my particular brand of A-positive.

    I have the same blood group but I’m fairly immune to midge bites. My wife on the other hand…

    I’ll collate my responses in this single post that people can just skip over, rather than spamming the sidebar.

    I find it more convenient to answer posts short sections at a time. If anyone objects to me having too many consecutive posts just let me know and I’ll try to reduce their number.

    CharlieM

    No. I believe that in Darwinian terms,bacteria are just some of the organisms that do outcompete us on a massive scale.

    Yikes! I’ve never been beaten to a hot dog by a bacterium! Well, I probably have, but there was still plenty left. I think an ecology primer might be in order, particularly the sense of ‘competition’.

    And which group would you consider to be the most successful in terms of reproduction numbers and biomass, bacteria or multicellular animals? From The biomass distribution on Earth

    We find that the kingdoms of life concentrate at different locations on the planet; plants (≈450 Gt C, the dominant kingdom) are primarily terrestrial, whereas animals ≈2 Gt C) are mainly marine, and bacteria (≈70 Gt C) and archaea (≈7 Gt C) are predominantly located in deep subsurface environments.

    What would be your justification for saying that we are more successful than bacteria in Darwinian terms?

    CharlieM

    I think that physics does show that the more dense the substance the more likely it is to fossilise.

    Allan Miller: Perhaps, but that’s a fair way from the ‘matter is condensed energy’ line you started with.

    There are no particles, there are only fields

    As this paper shows, experiment and theory imply that unbounded fields, not bounded particles, are fundamental. This is especially clear for relativistic systems, implying that it’s also true of nonrelativistic systems. Particles are epiphenomena arising from fields.

    The time has come for the importance of peripheral forces to be generally accepted. Our obsession with looking for fundamental answers by slicing reality into the ever smaller and separate has revealed, like an infinite line returning back to where it begins, an infinite expanse opening up from the smallest entities.

    CharlieM

    What about the pernicious political influence of Darwinism? A Darwinian extremist might argue that not vaccinating against a disease is a good thing because it will eliminate the weak members of the group.

    Whataboutery alert! Still, if I ever encountered such an individual, I would of course tell them they were talking shite, and that Darwinian evolution is not in any case a manifesto – descriptive not prescriptive.

    Or so it should be. But humans will be humans.

    CharlieM

    In my opinion the nucleus is the physical focus of the life (etheric) principle in eukaryotes. In transplanting the nucleus the life force is also transplanted.

    Aye, that’s handy – the smallest unit that’s been transferred successfully: that’s where the life force is located! And not much to do with those little thready things, merely used by the ‘life force’.

    Still, we have eliminated the cytoplasm. It’s a start.

    No. As long as there is molecular activity within the cytoplasm then it demonstrates life forces. Take a cutting from a plant and it may very well grow into a complete new plant, but chop off one of your fingers and what you will have is dead flesh and bone. Plants retain much more life force than we do.

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  40. CharlieM: What would be your justification for saying that we are more successful than bacteria in Darwinian terms?

    Allan didn’t say that. He said that there is no ecological competition between us and bacteria, which is absolutely correct. This too has come up before. If you do not work harder at restraining your inner guru this discussion will get very repetitive.

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  41. Allan Miller:

    CharlieM

    So we can agree that the nucleus is the seat of a strong regenerative life principle. But cells can retain living activity even after the nucleus along with the genome is ejected.

    They’ve lost the ‘regenerative’ part though…
    It is not necessary that the genome be constantly present, nor constantly active, in order for the genome to be the source of that which resides in the cytoplasm. It needs to make good losses, but cells are good for a few hours or days without. Depends on turnover.

    Depends on the life force. Stem cells and neurons have basically the same genomes but the life force is much stronger in stem cells. Nerve cells have had to give up their life forces in order to serve other purposes.

    CharlieM

    But genomes and proteomes are not separate in this way, they belong together and are a unity. And thus we get into paradoxes and contradictions when we try to think of one being the cause and the other the effect or them being related as in a means to an end.

    On the contrary, one evades a paradox: that for which your elaborate and ad hoc solution is the invention of a precursor Mind.

    Even without considering minds we can see that there is no such thing as naturally occurring DNA separate from other molecular complexes.

    CharlieM

    Living beings are not machines nor are they factories.

    Given my oft-expressed distaste for the over-extended metaphor, I’m surprised you think I might be of the opinion they were.

    So you disapprove of terms like ‘motor’ proteins because of their association with human designed machines?

    CharlieM

    Me: As you’d find if you consumed death cap fungus […]
    Charlie: Yes my actions will result in changes to gene expression. I also agree with that.
    Me: A spectacular piece of point-missing
    Charlie: What gets passed on are living processes. There are many external influences which can disrupt these processes.

    My point, though, was that the components of the cell which you invoke as ‘living process’ have a shelf-life measured in hours, as the ‘death cap’ experiment shows dramatically. They don’t have any persistence, but turn over continually, to be refreshed from the genome. Only that has the constancy required to provide the ultimate seat of regulation. Of course DNA turns over too, but it has a handy template-based mechanism of allowing the ‘message’ to outlast any given instance of the ‘medium’. It also scatters into trillions of novel copies of that same ‘message’. But, again because of that template mechanism, the informatic role persists. There is no equivalent means of ‘cytoplasmic’, or ‘nuclear-but-not-chromosomal’, persistence.

    So information gets passed on. Information that sits at a level above its physical carrier. DNA carries the information to make a huge variety of polymers. Organisms and cells use these polymers to suit their needs depending on their situation in time and space. One gene may be used in any number of ways and very many genes will be involved in most regulatory and constructive tasks. It’s like an orchestral score which can be arranged in any number of ways.

    CharlieM

    Charlie: Proteins are fundamental to all life.
    Me: All of modern life. But still, their sequences reside in DNA.
    Charlie: Fundamental to all known earthly life.

    Digging your heels in here suggests that you deny the possibility of a precursor system unless an example has left descendants of that type. That’s pretty restrictive – the only valid evolutionary processes are those that fail to eliminate competitors! – and sums up a lot of Creationist rhetoric, even though you would distance yourself from Creationism.

    I don’t see the need to speculate on a precursor system that relies on the chance interactions of lifeless chemicals. As it is my belief that lifeless matter is the product of living matter and not the other way round I have no need of such speculation..

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  42. CharlieM: Depends on the life force.

    Undefined term detected!

    Can CharlieM tell us anything of a life force? Units of measurement?

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  43. CharlieM:
    And which group would you consider to be the most successful in terms of reproduction numbers and biomass, bacteria or multicellular animals?

    Not a particularly relevant comparison. We’re here, they’re here … I would note in passing that eukaryotic cells are some 10,000 times the size of prokaryotes, and we have trillions of the things … But yeah, there are loads more apples than oranges. Shrug.

    How many DNA-miles in the prokaryote vs eukaryote worlds?

    What would be your justification for saying that we are more successful than bacteria in Darwinian terms?

    Do I say that? ‘Darwinian terms’ implies some kind of ecological competition for finite resources. We aren’t generally involved in such a contest with them.

    Allan Miller: Perhaps, but that’s a fair way from the ‘matter is condensed energy’ line you started with.

    Charlie: There are no particles, there are only fields

    That makes your original contention – “matter is condensed energy; early life wasn’t condensed enough to fossilise” – no less hideous a mangling of physics.

    Me: Whataboutery alert! Still, if I ever encountered such an individual, I would of course tell them they were talking shite, and that Darwinian evolution is not in any case a manifesto – descriptive not prescriptive.

    Charlie: Or so it should be. But humans will be humans.

    And Brexit means Brexit. You’ll need to do better than vague allusion to possibility.

    No. As long as there is molecular activity within the cytoplasm then it demonstrates life forces. Take a cutting from a plant and it may very well grow into a complete new plant, but chop off one of your fingers and what you will have is dead flesh and bone. Plants retain much more life force than we do.

    Pure hokum. Lizards’ tails are presumably a halfway house.

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  44. CharlieM:
    Depends on the life force. Stem cells and neurons have basically the same genomes but the life force is much stronger in stem cells.

    Not so. Epigenetics has channelled some cells to a particular setting that is constitutionally irreversible. Other cells remain totipotent.

    Me: On the contrary, one evades a paradox: that for which your elaborate and ad hoc solution is the invention of a precursor Mind.

    Charlie: Even without considering minds we can see that there is no such thing as naturally occurring DNA separate from other molecular complexes.

    So we can look at modern life and conclude there was never anything simpler? That is quite the logical fallacy.

    So you disapprove of terms like ‘motor’ proteins because of their association with human designed machines?

    No, I’m fine with it. My issue is with the over-extended metaphor.

    So information gets passed on. Information that sits at a level above its physical carrier. DNA carries the information to make a huge variety of polymers. Organisms and cells use these polymers to suit their needs depending on their situation in time and space.

    Organisms and cells are made of these polymers, or by them.

    One gene may be used in any number of ways and very many genes will be involved in most regulatory and constructive tasks. It’s like an orchestral score which can be arranged in any number of ways.

    Haha. You’ve been listening to Denis Noble again. The metaphor breaks down pretty rapidly, but anyway gene centrism does not depend on a 1:1 mapping of gene to trait, or product.

    Digging your heels in here suggests that you deny the possibility of a precursor system unless an example has left descendants of that type. That’s pretty restrictive – the only valid evolutionary processes are those that fail to eliminate competitors! – and sums up a lot of Creationist rhetoric, even though you would distance yourself from Creationism.

    Charlie: I don’t see the need to speculate on a precursor system …

    God yes, curse that intellectual curiosity! 🤣

    … that relies on the chance interactions of lifeless chemicals.

    RNA world is not strictly about ‘lifeless chemicals’, but simply about a prior state in which both inheritance and catalysis were performed by nucleic acid. Such hypothetical entities were as ‘alive’ as you or I, you protein chauvinist!

    As it is my belief that lifeless matter is the product of living matter and not the other way round I have no need of such speculation..

    Your belief hinges on your dismissing the possibility, leaving it rather self-sustaining and hermetically sealed. “Because I believe life needs protein, I don’t have to consider any scenario in which protein-free life could exist. What there is is all there was … once the Universe had made up its Mind, that is”.

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  45. Allan Miller,

    I feel that I’m getting caught up on minor details here and that this thread that I’ve hijacked is running away from me. I recommend a video by Johannes Jaeger, The Cell Is Not a Machine – Beyond Networks: The Evolution of Living Systems. As an example of some of the interesting stuff he brings up, In the video he explains that if you kill the DNA in the nuclei of drosophila embryo it will still self organise up to the point of gastrulation.

    He provides a complete course of video lectures here And I must point out that he denies that any external vital force is involved in development.

    I think that there is plenty to be taken from his work which will be worth a thread on its own, so I may very well start one.

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  46. Allan Miller: …Because genetics.

    Because integrated living processes which involve genetic manipulation.

    Living systems are not machines. A machine can be taken apart and reassembled because it is made of separate parts. Take a living nucleus apart and the result id dead matter.

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  47. Alan Fox:

    CharlieM: The pre-Cambrian earth could have been teeming with life that was so diaphanous that no trace of it has been left.

    The small shelly fauna (often neither small nor shelly) left fossil evidence as far back as the Ediacaran period from around 630 million years ago. The oldest uncontroversial evidence of life on Earth goes back 3.5 billion years. Hard parts bloom in the Cambrian, the proliferation of armoured plates and spikes perhaps due to an explosion in predatory species. Eyes, which also become widespread in the fossil record during the Cambrian period would also have been useful to predators and prey.

    But certainly, prior to the Ediacaran, fossil evidence, other than tracks and burrows, is sparse.

    The Cambrian is the time when many living forms became solid enough to leave fossil evidence. If is seems as though creatures like trilobites appeared from nowhere then it’s possible that their ancestors were too soft bodied to fossilise.

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  48. CharlieM: Because integrated living processes which involve genetic manipulation.

    It all starts with the genome.

    Name a level of control which does not root in the genome.

    Most of your phenotype consists of the residue of your last few meals. The residue of your last few meals is not ‘manipulating the genome’; it doesn’t have the persistence to form an organising principle; that constancy is provided by the genome, which ensures continuity and repeatability. That the genome does this via intermediates is not a refutation of this centrality.

    Living systems are not machines. A machine can be taken apart and reassembled because it is made of separate parts.

    Like I say, I’m not pushing that metaphor.

    Take a living nucleus apart and the result id dead matter.

    Because the genome relies upon its prior products for expression. Remove those products and it’s stuffed.

    Remove your blood and you’re dead matter. Does this mean blood is an organising principle?

    But I’ll say again: you keep confusing an evolutionary stance with a physiological one.

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